| Variant ID: vg1212987580 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12987580 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCAAATTTCTTATTTTTAAAATTTTATTTAAAATTCTTTATTTAAAAAAAACCTTTCCTTATTTATTTATTTACTTTCTAATTTTAAATTATTTTAATTA[A/T]
CCTTTAAAAATTATTTTAAATTTATTTGATTTACTTTATATCCCTTTAATTTTAAATTTATCGTTTAAAAACTTTTTTAAAATTTAATTATCCTTTAATT
AATTAAAGGATAATTAAATTTTAAAAAAGTTTTTAAACGATAAATTTAAAATTAAAGGGATATAAAGTAAATCAAATAAATTTAAAATAATTTTTAAAGG[T/A]
TAATTAAAATAATTTAAAATTAGAAAGTAAATAAATAAATAAGGAAAGGTTTTTTTTAAATAAAGAATTTTAAATAAAATTTTAAAAATAAGAAATTTGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.90% | 0.10% | 3.85% | 10.14% | NA |
| All Indica | 2759 | 85.10% | 0.00% | 3.26% | 11.60% | NA |
| All Japonica | 1512 | 84.80% | 0.30% | 5.95% | 8.93% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.00% | 4.46% | NA |
| Indica I | 595 | 85.50% | 0.00% | 4.54% | 9.92% | NA |
| Indica II | 465 | 73.80% | 0.00% | 4.09% | 22.15% | NA |
| Indica III | 913 | 93.90% | 0.00% | 1.10% | 5.04% | NA |
| Indica Intermediate | 786 | 81.40% | 0.00% | 4.33% | 14.25% | NA |
| Temperate Japonica | 767 | 74.40% | 0.70% | 10.95% | 13.95% | NA |
| Tropical Japonica | 504 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 2.49% | 2.90% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212987580 | A -> DEL | N | N | silent_mutation | Average:26.436; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg1212987580 | A -> T | LOC_Os12g22960.1 | upstream_gene_variant ; 4948.0bp to feature; MODIFIER | silent_mutation | Average:26.436; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg1212987580 | A -> T | LOC_Os12g22980.1 | upstream_gene_variant ; 2356.0bp to feature; MODIFIER | silent_mutation | Average:26.436; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| vg1212987580 | A -> T | LOC_Os12g22970.1 | intron_variant ; MODIFIER | silent_mutation | Average:26.436; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212987580 | 8.47E-08 | 1.14E-09 | mr1210 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1212987580 | 6.92E-08 | 1.10E-09 | mr1305 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1212987580 | 8.74E-06 | 9.48E-08 | mr1585 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1212987580 | 1.98E-07 | 3.19E-09 | mr1586 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1212987580 | NA | 1.44E-06 | mr1585_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |